Executing the Transformation

Overview

The Rhino Data Harmonization Engine (RhinoDHE) automatically converts Syntactic Mappings (and any associated Semantic Mappings) into reusable ETL workflows. These workflows run directly on your Rhino Client, in accordance with the principles of federated computing, to transform datasets from a source format into the defined target format.

Syntactic Mappings can be used to generate Data Harmonization Code Objects, which function like other Code Objects in Rhino FCP and can be executed remotely on a Rhino Client.

When a Data Harmonization Code Object is run, the Syntactic Mapping is applied to the input dataset, mapping source fields to target fields and applying any configured transformations. The resulting harmonized dataset is stored on the same Rhino Client and can then be used like any other dataset in Rhino FCP.

Prerequisites

• You must have the "Manage Data Mappings" permission.

• You must have the "Run Code on This Site" permission for the site on which the harmonization is to be run.

• The datasets that you want to harmonize must have been imported into FCP.

• The syntactic mapping you want to edit must exist.

• Any semantic mappings referenced by the syntactic mapping must exist.

Running a Data Harmonization Code Object

1

On Projects page, click on the project that contains your data mappings and datasets to select it.

2

Select the Code option from the navigation menu on the left-hand side of the page.

3

Locate the code object for your syntactic mapping. It has the same name as the mapping and type Data Harmonization.

A code object is automatically generated for each syntactic mapping created.

4

Select the Run button to the right of the code object to open the Run Settings page.

5

Select the Workgroup on which you want to run the code object.

6

Select the Input datasets.

There should be one for each input data schema.

An initial selection is already made for you, but you can change it by selecting the dataset dropdown menu and selecting a different dataset.

If there are no datasets that match a given source data schema, the text "NO OPTIONS" will appear. In this case, please close this dialog, import a matching dataset (from the Datasets menu option on the left-hand side navigation menu), then try again.

7

Select the Semantic Mappings.

One for each vocabulary or OMOP domain referenced by the syntactic mapping in different transformations.

An initial selection will already be made for you, but you can change it by clicking on the semantic mapping dropdown menu and selecting a different semantic mapping.

If there are no semantic mappings that match a given target vocabulary or OMOP domain, the text "NO OPTIONS" will appear. In this case, please close this dialog, create a matching semantic mapping (from the Data Mappings -> Semantic Mappings page), then try again.

8

Click Run to start the code run.

9

Click Code Runs from the menu on the left to see the code run entry.

You will see the status of the code run here.

Click on the status of the code run to see a detailed log from the code run (only visible if you have the required permissions.

10

Once the code has finished running, you will see the status change to Completed if the run completed successfully or Error if there was any error.

If the run completed successfully, you will see the number of output datasets under the Output Datasets field.

If there was an Error, click on the status to see the detailed logs with a description of the error encountered.

Troubleshooting

Symptom	Likely Cause	Resolution
NO OPTIONS for input dataset	No imported dataset matches the source schema	Import a dataset with the correct schema from the Datasets page
NO OPTIONS for semantic mapping	No semantic mapping matches the required vocabulary/domain	Create and approve a semantic mapping for that vocabulary/domain
Run status: Error	Configuration or data issue	Click the status to view detailed logs; review the error message for the affected field or transformation
Output dataset is empty	All rows failed transformation	Check error handling settings on transformations; review logs for per-row errors
Syntactic mapping is locked / cannot edit	The mapping was already run	Create a new version of the mapping — see [[Editing a Syntactic Mapping]]